Related papers: CSAW: a dynamical model of protein folding
Continuous-time random walks offer powerful coarse-grained descriptions of transport processes. We here microscopically derive such a model for a Brownian particle diffusing in a deep periodic potential. We determine both the waiting-time…
In this work we propose a model to describe the statistical fluctuations of the self-driven objects (species A) walking against an opposite crowd (species B) in order to simulate the regime characterized by stop-and-go waves in the context…
In colloidal systems, Brownian motion emerges from the massive separation of time and length scales associated to characteristic dynamics of the solute and solvent constituents. This separation of scales produces several temporal regimes in…
This is a rather personal review of the problem of self-avoiding walks and polygons. After defining the problem, and outlining what is known rigorously and what is merely conjectured, I highlight the major outstanding problems. I then give…
We introduce branching annihilating attracting walk (BAAW) in one dimension. The attracting walk is implemented by a biased hopping in such a way that a particle prefers hopping to a nearest neighbor located on the side where the nearest…
Systems living in complex non equilibrated environments often exhibit subdiffusion characterized by a sublinear power-law scaling of the mean square displacement. One of the most common models to describe such subdiffusive dynamics is the…
A global optimization method, conformational space annealing (CSA), is applied to study a 46-residue protein with the sequence B_9N_3(LB)_4N_3B_9N_3(LB)_5L, where B, L and N designate hydrophobic, hydrophilic, and neutral residues,…
A self-avoiding walk (SAW) is a path on a graph that visits each vertex at most once. The mean square displacement of an $n$-step SAW is the expected value of the square of the distance between the ending point and the starting point of an…
The spontaneous localization mechanism of collapse models induces a Brownian motion in all physical systems. This effect is very weak, but experimental progress in creating ultracold atomic systems can be used to detect it. In this paper,…
Monte Carlo simulations are performed to study structure and dynamics of a protein CoVE in random media generated by a random distribution of barriers at concentration c with a coarse-grained model in its native (low temperature) and…
A continuous time random walk (CTRW) is a random walk in which both spatial changes represented by jumps and waiting times between the jumps are random. The CTRW is coupled if a jump and its preceding or following waiting time are dependent…
Three-dimensional Monte Carlo simulations provide a striking confirmation to a recent theoretical prediction: the Brownian non-Gaussian diffusion of critical self-avoiding walks. Although the mean square displacement of the polymer center…
Monte Carlo simulations, using the PERM algorithm, of interacting self-avoiding walks (ISAW) and interacting self-avoiding trails (ISAT) in five dimensions are presented which locate the collapse phase transition in those models. It is…
Charge density wave (CDW) is a widely concerned emergent phenomenon in condensed matter physics. To establish a systematic understanding of CDW, we develop a diagrammatic self-consistent-field approach for cubic Holstein model employing…
Two closely related models of oriented self-avoiding walks (OSAWs) on a square lattice are studied. We use the pruned-enriched Rosenbluth method to determine numerically the phase diagram. Both models have three phases: a tight-spiral phase…
In this paper we are examining diffusion properties of stationary continuous-time Weierstrass walk (CTWW). We are showing it is a multi-phase representation of the L\'evy walk. The hierarchical spatial-temporal coupling, combined with…
It is well known that the weak limit of a suitably scaled continuous-time random walk (CTRW) is the Brownian motion. We investigate the convergence of certain patterned random matrices whose entries are independent CTRWs and their…
This paper describes continuously phase-modulated standing surface acoustic waves (CPM-SSAW) and its application for particle separation in multiple pressure nodes. A linear change of phase in CPM-SSAW applies a force to particles whose…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We consider scaled Brownian motion (sBm), a random process described by a diffusion equation with explicitly time-dependent diffusion coefficient $D(t) = D_0 t^{\alpha - 1}$ (Batchelor's equation) which, for $\alpha < 1$, is often used for…